Compressor Taking Too Long

Try turning/keeping the frame controls off. You're not re-sizing or re-timing. Also change to one pass not multi-pass. Frame controls "Best Setting" and multi-pass add significant time to compressions. Do a test and compare with your previous settings and it should look fine.

With all your frame controls at best, I'm not really sure what I'd view as the outlier – 40 minutes or 50 hours. Out of curiosity, I tried a piece of test footage on a similarly specced machine and got a 120:1 result (extrapolating, that works out to approximately 10 hours for a 5 minute source file.) To quote the manual,

Important: Using all Best settings may result in unexpectedly long processing times.

However, hard to say why it might vary so much…perhaps progressive source material in one and interlaced in another…possibly one or more adjustments set to better? As I indicated, with those settings, I think I would be as surpised by the 40 minute encode

Anyway, the difference in processing time between better and best is huge. Try dialing it down a notch and see what it does to your times and to quality.

In addition to the other advice offered, you might also improve processing time by setting up Compressor to use multiple cores. Tutorial: http://www.digitalrebellion.com/blog/posts/using_compressor_with_multiple_cores. html

Mmmmm...

The best thing to do is to use ProRes (first) to deinterlace your video before you compress to H.264. H.264 will read the Frame Control for each pass, adding to the time for compressing. Also setup the QMaster to to utilize all of your cores, this will cut the encoding time for both ProRes and H.264.

To save time between the ProRes and H.264 encoding you can setup Chaining Job option in Compressor. This will encode the PreRes first and then will automatically encode it to H.264. Type CHAINING in the Compressor Help Menu for more info.

As for setting everything to best in Frame Control. If there isn't a change in the video, for example resizing. Frame Control will not use the resizing option no matter what setting you use, bypassing it.

Here is how I determine if I need to deinterlace a video. In the Preview widow I scrub the video look for interlacing artifacts. If I don't see any I set the video to progressive and don't use Frame Control to deinterlace the video.

Sorry, missed the that your source was interlaced. In that case turn frame controls on and change "Output Fields" to "Progressive" and "Deinterlace" to "Fast (Line averaging)" or "Better (Motion adaptive)" depending if your video has lot's of motion. "Better (Motion adaptive)" may take a little longer but not too drastic. Test both and see which works for you. There's also "JES Deinterlacer" that some people swear by that you can de-interlace before compression and best of all it's free.

Use ProRes to delinterlace the video too. Take that video and compress to H.264.

I did a test and a one minute video (1920x1080i) with best settings in Frame Control took about 7 minutes to encode.